This web page was produced as an assignment
for an undergraduate course at Davidson College.

My Favorite Yeast Genes: PCP1 and
YGR102C

Introduction

PCP1(also referred to by the systematic name YGR101W) and
YGR102C are two genes of the organism Saccharomyces
cerevisiae, commonly known as Baker's yeast. They are located within
a small region in chromosome VII. While the function of
PCP1 is well known, the nearby gene YGR102C is a hypothetical ORF that has not
yet been annotated. The chromosomal map below, from the Stanford
Saccharomyces Genome Database, shows the locations of the two genes. The
chromosomal coordinates for PCP1 are 693364 to 694404 and the chromosomal
coordinates for the YGR102C are 695136 to 694585.

Click here
for the genomic DNA sequence. It consists of 552 base pairs.

Click
here for the Entrez-Protein link for YGR102C. It is 183 residues long.

Predictions on the nature of the protein can be made using
Kyte-Doolittle hydropathy plot.

Figure 2: Kyte-Doolittle Plot

When the window size is 19, no parts of the
protein have a hydropathy score greater than 1.8. Thus we can deduce that the
protein does not have any trans-membrane regions but may be located somewhere in
the cytoplasm.

We can also compare the genomic DNA and protein sequences to
known sequences of other genes.

The potential matching protein was an unnamed yeast protein
product (accession number: CAA97107).
It is encoded by the gene YGR103W, the same one that BLASTn yielded.

Click here
to learn more about YGR103W at the SGD. Also called NOP7, it is a nucleolar
protein present in purified ribosome assembly intermediates. It is required for
rRNA processing; required for essential steps leading to synthesis of 60S
ribosomal subunits. However, its molecular function is unknown.
Notice in Figure 1 that NOP7 is located in close proximity to YGR102C on the
same chromosome.

Since YGR102C has a DNA sequence similar to that of NOP7, and it
also encodes a protein that is very similar to the one encoded by NOP7, we can
hypothesize that YGR102C is a nucleolar protein with a potentially similar
function.